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Molecule Parameter List for CaM_dash_Ca3

The statistics table lists the distribution of a molecule acting either as a substrate, product, enzyme or as a molecule within the network. The text color of a molecule is highlighted by color.

Statistics

CaM_dash_Ca3 participated as	Molecule	Sum total of	Enzyme	Substrate of an enzyme	Product of an enzyme	Substrate in Reaction	Product in Reaction
No. of occurrences	1	0	0	0	0	2	1

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
Differential syn thesis of mRNA	95	Network	kinetics,  compartment_1,  compartment_2
The model consists of three major pathways: Calcium-calmodulin dependent protein kinase IV (CaMKIV), Mitogen-activated protein kinase (MAPK) and Protein Phosphatase 1 (PP1). Each of these converged on CREB activation. We also modeled further interactions with Transducer of regulated CREB activity 1 (TORC1) and the protein kinase A (PKA) pathway.

CaM_dash_Ca3 acting as a Molecule in  Differential synthesis of mRNA Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
CaM_dash_Ca3	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	0	1000	No

CaM_dash_Ca3 acting as a Substrate in a reaction in  Differential synthesis of mRNA Network

Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated. Kd for higher order reaction are not consider.

	Name	Accession Name	Pathway Name	Kf	Kb	Kd	tau	Reagents
1	CaM_dash_Ca3_ dash_bind_dash_ Ca	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	0.465 (uM^-1 s^-1)	10 (s^-1)	Kd(bf) = 21.5051(uM)	-	Substrate Ca CaM_dash_Ca3 Product CaM_dash_Ca4
	Use K3 = 21.5 uM here from Stemmer and Klee table 3. kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10
2	CaMCa3_dash_ bind_dash_CaNAB	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	2.238 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 0.4468(uM)	-	Substrate CaM_dash_Ca3 CaNAB_dash_Ca4 Product CaMCa3_dash_ CaNAB

CaM_dash_Ca3 acting as a Product in a reaction in  Differential synthesis of mRNA Network

Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated. Kd for higher order reaction are not consider.

Name	Accession Name	Pathway Name	Kf	Kb	Kd	tau	Reagents
CaM_dash_Ca2_ dash_bind_dash_ Ca	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	3.6001 (uM^-1 s^-1)	10 (s^-1)	Kd(bf) = 2.7777(uM)	-	Substrate Ca CaM_dash_Ca2 Product CaM_dash_Ca3
K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10